On December 2, 1998, Ferentz was hired as Iowa's 26th head football coach to replace the retiring Hayden Fry.[1] The team struggled during Ferentz's first two seasons with a combined 4–19 record, but the Hawkeyes earned their first bowl bid of the Ferentz era after a 7–5 season in 2001. They beat Texas Tech in the Alamo Bowl, 19–16.

Ferentz had to deal with multiple injuries to the Hawkeyes' running backs and the death of his father, John, during the 2004 season. Nevertheless, the Hawkeyes compiled a 9–2 regular season record, sharing the Big Ten Conference championship with Michigan after a 30–7 victory over Wisconsin on November 20. For the second time in three seasons, Ferentz was named the Big Ten Conference Coach of the Year. On January 1, 2005, they defeated LSU, 30–25, after a thrilling 56-yard touchdown pass from Drew Tate to Warren Holloway as time expired in the Capital One Bowl. This gave Ferentz his third straight ten-win season with the Hawkeyes and another #8 national ranking.

The Hawkeyes went 7–4 during the 2005 regular season. After early-season losses to Iowa State and Ohio State and close losses to Michigan and Northwestern, they finished the season with wins over Wisconsin and Minnesota to earn a second trip to the Outback Bowl to face Florida on January 2, 2006. This time, however, the Gators got a measure of revenge for their loss two years earlier, as the Hawkeyes lost to Florida, 31–24. Much was said about the officiating in this game, as there were 13 missed or bad calls made against the Hawkeyes that directly influenced the outcome. The NCAA made an official acknowledgment of this issue.

Iowa started the 2006 season strong, winning their first four games before losing to top-ranked Ohio State. After a 5–1 start, however, the Hawkeyes collapsed down the stretch, losing five of their last six games. Iowa suffered shocking losses to Northwestern and Indiana and lost rivalry games with Wisconsin and Minnesota. The Hawkeyes finished the regular season with a 6–6 record and accepted an invitation to the 2006 Alamo Bowl, Iowa's sixth straight bowl game. Playing as nine-point underdogs to defending national champions Texas, Iowa lost the Alamo Bowl by a score of 26–24.

In 2007, Ferentz' Hawkeyes started 2–4 and lost their first three conference games. An upset victory over Illinois ended a nine-game conference losing streak for Iowa, and the Hawkeyes closed out the Big Ten season by winning their last three conference games. However, a disappointing loss in the season finale to Western Michigan dropped the Hawkeyes' season record to 6–6. Though Iowa was bowl-eligible, the Hawkeyes did not receive a bowl bid, snapping Iowa's streak of six consecutive bowl appearances.

In 2008, Ferentz and the Hawkeyes started out strong with victories over his old team, Maine, Florida International, and rival Iowa State, but close losses to Pitt, Northwestern, and Michigan State left Iowa with a 3–3 record. Iowa then went on to win five of their next six games, including a 24–23 upset of #3 ranked and undefeated Penn State. After finishing the regular season at 8–4, Iowa accepted an invitation to the Outback Bowl where they defeated the South Carolina Gamecocks, 31–10.

Ferentz and Ohio State coach Jim Tressel talk on the field before their teams played on November 14, 2009.

The 2009 Hawkeye football team got off to the best start in school history up to that point. Narrow home victories over Northern Iowa and Arkansas State coupled with double digit road wins over Penn State and Wisconsin fueled a 7–0 start. Ferentz' 2009 Hawks became the first Iowa team to win eight games to start a season by winning at Michigan State, 15–13, with a touchdown pass on the final play of the game. After defeating Indiana to run their record to 9–0, the Hawks lost quarterback Ricky Stanzi to injury in an upset loss to Northwestern. Iowa then lost the de facto Big Ten championship game at Ohio State, 27–24, in overtime. The Hawkeyes shut out Minnesota, 12–0, to finish the regular season with a 10–2 record and were selected for their second BCS bowl game under Ferentz by being invited to the 2010 Orange Bowl. Iowa defeated Georgia Tech, 24–14, to earn the school's first BCS bowl win and their first victory in a BCS-level bowl since the 1959 Rose Bowl. Iowa finished with an 11–2 record that tied the school record for victories in a season and the Hawkeyes earned #7 rankings in both the AP Poll and Coaches Poll, their highest finish since the 1960 season.[2]

Following three mediocre seasons in which Iowa went just a combined 19-19, the 2015 season proved to be one of the best in university history. Iowa went undefeated in the regular season and recorded 12 wins, the most in school history. Additionally, a team that went 0-4 in trophy games the year before, went 4-0 and won the Big Ten Conference West championship, the first in school history. Ferentz was also named Big Ten coach of the year for the fourth time while at Iowa. The Hawkeyes fell 16-13 in the 2015 Big Ten Football Championship Game against Michigan State. Despite the loss, the Hawkeyes accepted an invitation to the 2016 Rose Bowl, Ferentz's third Rose Bowl with Iowa, first as head coach, and it marks the first trip to Pasadena for the Hawkeyes in 25 years. In the Rose Bowl, the Hawkeyes were throttled, 45-16, by a Christian McCaffery led Stanford team.
With their latest Rose Bowl defeat, the Hawkeyes fell to 0-4, with a combined score of 164-78, since their last victory in 1959.

In 2016, Iowa suffered numerous injuries which derailed them in the earlier part of the season. However, they finished strong beating #3 Michigan, and prevailed over #16 Nebraska, finishing with an 8-4 record. The Iowa offensive line was awarded the Joe Moore Award. This award was especially significant because Moore was a lifelong mentor to Ferentz, and the team had to overcome a great deal to win it. Iowa was selected to play in the Outback Bowl for the fifth time under Ferentz, where they lost to the Florida Gators 30-3. Following the loss to the Gators the Hawkeyes fell to 0-5 in their last five bowl games, getting outscored 172-75 in those contests.

The 2017 season was almost a carbon copy of the previous season. Iowa got off to a great start but was again plagued with several injuries. The team went undefeated in non-conference play and all but two of their Big Ten loses were by just one score (38-14 vs. Wisconsin, 24-15 vs. Purdue). Like the prior season, Iowa went 3-1 in trophy games, and finished with eight wins. They were also able to beat #3 Ohio State for the first time since 2004. Iowa played in the Pinstripe Bowl, the 15th bowl under Ferentz. After trailing early, the Hawkeyes dominated the second half and won their first bowl game since 2010. The victory tied Hayden Fry in Iowa career wins (143), and surpassed his number of bowl wins at the university.

The 2018 season will undoubtedly be remembered for close Big Ten Conference loses that cost the Hawkeyes another trip to Indianapolis. Iowa started strong, winning out in non-conference, and once again was able to keep three of the four rivalry trophies in Iowa City. However, heartbreaking loses that occurred in three consecutive weeks defined the season. Iowa played in the Outback Bowl for the sixth time, holding on to defeat Mississippi State 27-22 for Ferentz's fifth January bowl win and eighth overall bowl victory.

As of October 2018, Ferentz is 14-6 versus Big Ten rival Minnesota and 11-9 versus in-state rival Iowa State, though his predecessor went 16-4 against their in-state rival. He also has a winning record against every Big Ten team that has been in the league before 2012 except for Ohio State and Wisconsin. Ferentz notched his 100th career win at Iowa with a double-overtime victory over the Michigan State Spartans in East Lansing on October 13, 2012. He became the all-time wins leader in school history, (144) with a victory over Northern Illinois on September 1, 2018, and has led Iowa to 16 bowl games, more bowls than any other Iowa coach. Later that season Ferentz recorded his 150th Iowa career win with a blowout triumph over Big Ten foe Illinois on November 17, 2018. When Joe Paterno was fired from Penn State in 2011 Ferentz became the dean of Big Ten football coaches, as the longest tenured coach in the respective sport. With the retirement of Virginia Tech coach Frank Beamer after the 2015 season, Ferentz became tied with Bob Stoops for the longest tenured head coach at the FBS level. In June 2017, Ferentz became the longest tenured coach with the sudden retirement of Bob Stoops.

Several major college and NFL teams have considered Ferentz as a candidate for their head coaching jobs. However, Ferentz has publicly declined any interest in other coaching positions, opting to stay at Iowa. On February 12, 2009, Ferentz and Iowa athletics director Gary Barta agreed to a new contract extension that keeps Ferentz at Iowa until 2020.[3]

On January 2, 2006 the head coaches of five NFL teams, Green Bay, St. Louis, Houston, New Orleans, and Minnesota, were fired. There was renewed speculation that Ferentz would be offered a head coaching job with one of those professional franchises. But such speculation was soon put to rest when Ferentz stated that he was still happy with his job at Iowa, and that he had no plans to leave.[4]

On June 2, 2006, Ferentz became the highest paid coach in the Big Ten and third highest in college football when he was given a restructured contract that boosted his annual salary to $2.7 million.[5]

Following the 2006 NFL season, rumors circulated that Ferentz may have been in consideration for the Pittsburgh Steelers' head coaching job after Bill Cowher stepped down. However, before Cowher's departure, Ferentz was asked about his possible interest in the position, and stated: "I know that staff pretty well and they've got some good guys in that building. My guess is that's where they would go. But I’m not interested, and I doubt they are, either. I’ve got a great job right here."[6] The Steelers job eventually went to Mike Tomlin.

In January 2009, rumors surfaced citing Ferentz as a potential candidate to be hired as head coach in place of Herman Edwards soon after the hiring of former New England Patriots VP of Player Personnel Scott Pioli as the new GM of the Kansas City Chiefs. However, the Chiefs eventually hired Todd Haley, and Ferentz received a contract extension to remain at Iowa through 2020. In December 2011, rumors again surfaced citing Ferentz as a potential candidate to replace Haley. Similar rumors surfaced a year later in December 2012. Ferentz has said that there was no reason to leave Iowa as Iowa has everything he needed.

Ferentz and his wife, Mary, have five children: Brian, Kelly, Joanne, James, and Steven.[9]Brian was a starting offensive lineman on the 2005 Iowa football team, a practice squad player for the Atlanta Falcons and New Orleans Saints. Since the 2012 season, Brian has served as the offensive line coach for Iowa. In January 2017, Brian was named the offensive coordinator.[10] From 2008 – 2011, Brian was a coach for the New England Patriots, including one record-breaking season as Tight Ends Coach.[11]James was a second team All-Big Ten center in 2012.[12] Additionally, James became a Super Bowl Champion with the Denver Broncos following the 2015 season. Kelly earned her JD and MHA degrees from Iowa in 2010–11 and Joanne earned her bachelor's degree from Iowa in 2010.[13] Steven graduated in 2017 and was a member of the football team.[14][15][16]

Ferentz has developed a reputation as a developer of talent during his tenure at Iowa. Since 1999, Iowa has routinely taken walk on, two, and three star talent and developed them into NFL prospects. During his tenure, Iowa has had 66 players drafted into the NFL, including seven first round picks, all while consistently recruiting high school players who are not desired by big time college programs. Iowa offensive linemen in particular are highly sought after by NFL teams, citing their work ethic and technical proficiency as being highly developed.